One of the problems in intensive aquaculture system is the the accumulation of waste in the water and sediment. Aquaculture wastes are discharged into the water in form of solids and dissolved nutrients which mostly consisted of nitrogen and phosphorus. The purpose of this study was to study the dynamics of total nitrogen and phosphorus in an intensive aquaculture media supplied with water hyacinth and probiotics (Pseudomonas aeruginosa and Achromobacter insuavis). The study was designed using a completely randomized design with treatment combinations of water hyacinth with probiotic (A), water hyacinth (B), and probiotic (C). Each treatment consisted of three replications. The seeds of snakehead used had body length of 14.74 ± 0.01 cm and weight 25.53 ± 0.09 g, stocked in ponds with stocking density of 175 individuals/pond (50 individuals/m3). During 90 days of rearing, the fish were fed with pellet with protein content of 30%. The amount of feeding was 5% of the biomass with feeding frequency of four times a day (morning, afternoon, evening, and night). The results showed that the produced nitrogen and phosphorus in the snakehead cultivation were distributed to water hyacinth, sediment, water, and fish. Water hyacinth absorbed most of the nitrogen and phosphorus compared to water, fish, and sediment. Higher specific growth rate (4.37 ± 0.01%/day) and biomass (1.88 ± 0.01 g) of snakehead were achieved in combination of water hyacinth and probiotic treatment. These results can be used as a basis for the management of nitrogen and phosphorus wastes in an intensive fish farming.